메뉴 건너뛰기




Volumn 10, Issue , 2009, Pages 354-

Gene ARMADA: An integrated multi-analysis platform for microarray data implemented in MATLAB

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMIC ANALYSIS; DIFFERENTIALLY EXPRESSED GENE; MICROARRAY DATA ANALYSIS; MICROARRAY DATA SETS; OLIGONUCLEOTIDE ARRAYS; SEAMLESS INTEGRATION; STANDALONE APPLICATIONS; STATISTICAL SELECTION;

EID: 70450260624     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-354     Document Type: Article
Times cited : (38)

References (37)
  • 2
    • 33746683125 scopus 로고    scopus 로고
    • Analysis of microarray experiments of gene expression profiling
    • 10.1016/j.ajog.2006.07.001, 2435252, 16890548
    • Tarca AL, Romero R, Draghici S. Analysis of microarray experiments of gene expression profiling. American journal of obstetrics and gynecology 2006, 195(2):373-388. 10.1016/j.ajog.2006.07.001, 2435252, 16890548.
    • (2006) American journal of obstetrics and gynecology , vol.195 , Issue.2 , pp. 373-388
    • Tarca, A.L.1    Romero, R.2    Draghici, S.3
  • 3
    • 33745407776 scopus 로고    scopus 로고
    • The microarray data analysis process: from raw data to biological significance
    • 10.1016/j.nurx.2006.05.005, 16815220
    • Olson NE. The microarray data analysis process: from raw data to biological significance. NeuroRx 2006, 3(3):373-383. 10.1016/j.nurx.2006.05.005, 16815220.
    • (2006) NeuroRx , vol.3 , Issue.3 , pp. 373-383
    • Olson, N.E.1
  • 5
    • 33645804408 scopus 로고    scopus 로고
    • Mayday--a microarray data analysis workbench
    • 10.1093/bioinformatics/btl070, 16500939
    • Dietzsch J, Gehlenborg N, Nieselt K. Mayday--a microarray data analysis workbench. Bioinformatics (Oxford, England) 2006, 22(8):1010-1012. 10.1093/bioinformatics/btl070, 16500939.
    • (2006) Bioinformatics (Oxford, England) , vol.22 , Issue.8 , pp. 1010-1012
    • Dietzsch, J.1    Gehlenborg, N.2    Nieselt, K.3
  • 6
    • 12344315879 scopus 로고    scopus 로고
    • Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data
    • 10.1093/bioinformatics/bth424, 15271778
    • Knowlton N, Dozmorov IM, Centola M. Microarray Data Analysis Toolbox (MDAT): for normalization, adjustment and analysis of gene expression data. Bioinformatics (Oxford, England) 2004, 20(18):3687-3690. 10.1093/bioinformatics/bth424, 15271778.
    • (2004) Bioinformatics (Oxford, England) , vol.20 , Issue.18 , pp. 3687-3690
    • Knowlton, N.1    Dozmorov, I.M.2    Centola, M.3
  • 7
    • 4444327079 scopus 로고    scopus 로고
    • ArrayNorm: comprehensive normalization and analysis of microarray data
    • 10.1093/bioinformatics/bth174, 15073026
    • Pieler R, Sanchez-Cabo F, Hackl H, Thallinger GG, Trajanoski Z. ArrayNorm: comprehensive normalization and analysis of microarray data. Bioinformatics (Oxford, England) 2004, 20(12):1971-1973. 10.1093/bioinformatics/bth174, 15073026.
    • (2004) Bioinformatics (Oxford, England) , vol.20 , Issue.12 , pp. 1971-1973
    • Pieler, R.1    Sanchez-Cabo, F.2    Hackl, H.3    Thallinger, G.G.4    Trajanoski, Z.5
  • 8
    • 49049104614 scopus 로고    scopus 로고
    • MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
    • 10.1186/gb-2008-9-7-r118, 2530872, 18652698
    • Chu VT, Gottardo R, Raftery AE, Bumgarner RE, Yeung KY. MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis. Genome biology 2008, 9(7):R118. 10.1186/gb-2008-9-7-r118, 2530872, 18652698.
    • (2008) Genome biology , vol.9 , Issue.7
    • Chu, V.T.1    Gottardo, R.2    Raftery, A.E.3    Bumgarner, R.E.4    Yeung, K.Y.5
  • 9
    • 62849123277 scopus 로고    scopus 로고
    • PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data
    • 10.1186/1471-2105-10-16, 2657788, 19134227
    • Martin-Requena V, Munoz-Merida A, Claros MG, Trelles O. PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data. BMC Bioinformatics 2009, 10:16. 10.1186/1471-2105-10-16, 2657788, 19134227.
    • (2009) BMC Bioinformatics , vol.10 , pp. 16
    • Martin-Requena, V.1    Munoz-Merida, A.2    Claros, M.G.3    Trelles, O.4
  • 12
    • 79951607984 scopus 로고    scopus 로고
    • FlexArray: A statistical data analysis software for gene expression microarrays
    • FlexArray: A statistical data analysis software for gene expression microarrays. , http://genomequebec.mcgill.ca/FlexArray
  • 13
    • 34447319661 scopus 로고    scopus 로고
    • IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform
    • 10.1093/bioinformatics/btm101, 17384020
    • Schultze JL, Eggle D. IlluminaGUI: graphical user interface for analyzing gene expression data generated on the Illumina platform. Bioinformatics (Oxford, England) 2007, 23(11):1431-1433. 10.1093/bioinformatics/btm101, 17384020.
    • (2007) Bioinformatics (Oxford, England) , vol.23 , Issue.11 , pp. 1431-1433
    • Schultze, J.L.1    Eggle, D.2
  • 14
    • 33645287677 scopus 로고    scopus 로고
    • AffylmGUI: a graphical user interface for linear modeling of single channel microarray data
    • 10.1093/bioinformatics/btl025, 16455752
    • Wettenhall JM, Simpson KM, Satterley K, Smyth GK. affylmGUI: a graphical user interface for linear modeling of single channel microarray data. Bioinformatics (Oxford, England) 2006, 22(7):897-899. 10.1093/bioinformatics/btl025, 16455752.
    • (2006) Bioinformatics (Oxford, England) , vol.22 , Issue.7 , pp. 897-899
    • Wettenhall, J.M.1    Simpson, K.M.2    Satterley, K.3    Smyth, G.K.4
  • 17
    • 0035875553 scopus 로고    scopus 로고
    • Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects
    • 10.1093/nar/29.12.2549, 55725, 11410663
    • Tseng GC, Oh MK, Rohlin L, Liao JC, Wong WH. Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects. Nucleic acids research 2001, 29(12):2549-2557. 10.1093/nar/29.12.2549, 55725, 11410663.
    • (2001) Nucleic acids research , vol.29 , Issue.12 , pp. 2549-2557
    • Tseng, G.C.1    Oh, M.K.2    Rohlin, L.3    Liao, J.C.4    Wong, W.H.5
  • 18
    • 0002552781 scopus 로고
    • Local regression models
    • Wadsworth & Brooks/Cole Dormand, J.R, Chambers JM, Hastie TJ
    • Cleveland WS, Grosse E, Shyu WM. Local regression models. Statistical Models in S 1992, Wadsworth & Brooks/Cole Dormand, J.R, Chambers JM, Hastie TJ.
    • (1992) Statistical Models in S
    • Cleveland, W.S.1    Grosse, E.2    Shyu, W.M.3
  • 19
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 10.1093/bioinformatics/19.2.185, 12538238
    • Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (Oxford, England) 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
    • (2003) Bioinformatics (Oxford, England) , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 20
    • 0003854151 scopus 로고
    • Exploratory data analysis
    • Reading, MA: Addison-Wesley
    • Tukey JW. Exploratory data analysis. 1977, Reading, MA: Addison-Wesley.
    • (1977)
    • Tukey, J.W.1
  • 22
    • 0036376993 scopus 로고    scopus 로고
    • Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments
    • Dudoit S, Yang YH, Callow MJ, Speed TP. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 2002, 12:111-140.
    • (2002) Statistica Sinica , vol.12 , pp. 111-140
    • Dudoit, S.1    Yang, Y.H.2    Callow, M.J.3    Speed, T.P.4
  • 23
    • 0001677717 scopus 로고
    • Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing
    • Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing. J R Statist Soc 1995, 57:289-300.
    • (1995) J R Statist Soc , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 25
    • 17944394324 scopus 로고    scopus 로고
    • Fuzzy C-means method for clustering microarray data
    • 10.1093/bioinformatics/btg119, 12761060
    • Dembele D, Kastner P. Fuzzy C-means method for clustering microarray data. Bioinformatics (Oxford, England) 2003, 19(8):973-980. 10.1093/bioinformatics/btg119, 12761060.
    • (2003) Bioinformatics (Oxford, England) , vol.19 , Issue.8 , pp. 973-980
    • Dembele, D.1    Kastner, P.2
  • 26
    • 0035532141 scopus 로고    scopus 로고
    • Estimating the number of clusters in a data set via the gap statistic
    • Tibshirani R, Walther G, Hastie T. Estimating the number of clusters in a data set via the gap statistic. J R Statist Soc 2001, 63(2):411-423.
    • (2001) J R Statist Soc , vol.63 , Issue.2 , pp. 411-423
    • Tibshirani, R.1    Walther, G.2    Hastie, T.3
  • 27
    • 0033657261 scopus 로고    scopus 로고
    • Principal components analysis to summarize microarray experiments: application to sporulation time series
    • 2669932, 10902193
    • Raychaudhuri S, Stuart JM, Altman RB. Principal components analysis to summarize microarray experiments: application to sporulation time series. Pac Symp Biocomput 2000, 455-466. 2669932, 10902193.
    • (2000) Pac Symp Biocomput , pp. 455-466
    • Raychaudhuri, S.1    Stuart, J.M.2    Altman, R.B.3
  • 28
    • 0003991806 scopus 로고    scopus 로고
    • Statistical Learning Theory
    • New York: Wiley
    • Vapnik VN. Statistical Learning Theory. 1998, New York: Wiley.
    • (1998)
    • Vapnik, V.N.1
  • 29
    • 84870686740 scopus 로고    scopus 로고
    • OSU SVM Toolbox for MATLAB
    • OSU SVM Toolbox for MATLAB. , http://sourceforge.net/projects/svm/
  • 30
    • 84871670892 scopus 로고    scopus 로고
    • LIBSVM: a library for support vector machines
    • LIBSVM: a library for support vector machines. , http://www.csie.ntu.edu.tw/~cjlin/libsvm/
  • 31
    • 0036578644 scopus 로고    scopus 로고
    • GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
    • 10.1038/ng0502-19, 11984561
    • Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nature genetics 2002, 31(1):19-20. 10.1038/ng0502-19, 11984561.
    • (2002) Nature genetics , vol.31 , Issue.1 , pp. 19-20
    • Dahlquist, K.D.1    Salomonis, N.2    Vranizan, K.3    Lawlor, S.C.4    Conklin, B.R.5
  • 33
    • 0012887049 scopus 로고    scopus 로고
    • Imaging spectrometry: basic principles and prospective applications
    • Dordrecht; Boston: Kluwer Academic Publishers
    • Meer F, Jong S. Imaging spectrometry: basic principles and prospective applications. 2001, Dordrecht; Boston: Kluwer Academic Publishers.
    • (2001)
    • Meer, F.1    Jong, S.2
  • 36
    • 55749101777 scopus 로고    scopus 로고
    • Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis
    • 10.1101/gad.501108, 2577787, 18981474
    • Nielsen R, Pedersen TA, Hagenbeek D, Moulos P, Siersbaek R, Megens E, Denissov S, Borgesen M, Francoijs KJ, Mandrup S. Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev 2008, 22(21):2953-2967. 10.1101/gad.501108, 2577787, 18981474.
    • (2008) Genes Dev , vol.22 , Issue.21 , pp. 2953-2967
    • Nielsen, R.1    Pedersen, T.A.2    Hagenbeek, D.3    Moulos, P.4    Siersbaek, R.5    Megens, E.6    Denissov, S.7    Borgesen, M.8    Francoijs, K.J.9    Mandrup, S.10


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.